... If you're going to do a bunch of them in batch, probably downloading the GO ontology release (http://geneontology.org/page/download-ontology) and then extracting out the information you want through a small script would be the best way.
If you have few enough you can do them by hand, I would say ju ...

... If you want to visualize the VCFs you created, try IGV (http://www.broadinstitute.org/igv/).
You've basically hit the end of the automatic pipeline where you can run one tool after another and have something meaningful without designing a bioinformatics experiment. Mutect2 did the equivalent of ...

... Do you have the raw data or is the only data you have this bed file? Are these small regions adjacent to each other? It's possible that each small region has a certain signal, and multiple small regions together are showing the full broad peak (which could have a variety of different signal streng ...

... I would suggest R. You can generate lots of different good visualizations there. It is free and pretty easy to use (although a little bit of a learning curve so hang in there). You just load the data you want and then tell it what to plot and how. You can do lots of customization and then fix is ...

... I see it in src/SeqAn-1.4.2/seqan/store/store_io_gff.h and src/tophat-fusion-post (although I think the second isn't relevant in this case). In the header file it looks like it is trying to match some type of key, which would make sense that it is looking in the info column of the GTF. I have to s ...